N2 Bond Research Articles

From singlet R2Si silylene to triplet R2Si═Si ground state by DFT

AbstractIn a quest for triplet silylenes, two sets of singlet monosilylenes (R2Si), including 1,4‐di(R)tetrazol‐5‐silaylidenes (1‐5) and 1,3‐di(R)tetrazol‐5‐silaylidenes (6‐10), are converted to their corresponding triplet R2Si═Si (1′‐10′) by taking advantage of an additional electropositive silicon atom that promotes conversion of singlet to triplet, at B3LYP/6‐311++G** level of theory, where R = H, methyl, ethyl, i‐propyl, and t‐butyl. Interestingly, every triplet 1′t‐10′t (R2Si═Si) is more stable than its corresponding singlet 1′s‐10′s. Also, every singlet R2Si═Si exhibits a higher nucleophilicity (N) and appears with a narrower singlet‐triplet energy difference (ΔES‐T) and smaller band gap (ΔΕHOMO‐LUMO) than its corresponding singlet R2Si. For singlet R2Si═Si, hydrogenation energies (ΔH) and N─Si─N angle increase as the size of R increases. Both asymmetric 6‐10 and 6′‐10′ exhibit higher N than their corresponding symmetric 1‐5 and 1′‐5′, respectively. Also, a wider N1─Si─N4 bond angle is encountered for R2Si═Si compared with R2Si.

What Is the Structure of the E4 Intermediate in Nitrogenase?

Nitrogenase is the only enzyme that can cleave the strong triple bond in N2. The active site contains a complicated MoFe7S9C cluster. It is believed that it needs to accept four protons and electrons, forming the E4 state, before it can bind N2. However, there is no consensus on the atomic structure of the E4 state. Experimental studies indicate that it should contain two hydride ions bridging two pairs of Fe ions, and it has been suggested that both hydride ions as well as the two protons bind on the same face of the cluster. On the other hand, density functional theory (DFT) studies have indicated that it is energetically more favorable with either three hydride ions or with a triply protonated carbide ion, depending on the DFT functional. We have performed a systematic combined quantum mechanical and molecular mechanical (QM/MM) study of possible E4 states with two bridging hydride ions. Our calculations suggest that the most favorable structure has hydride ions bridging the Fe2/6 and Fe3/7 ion pairs. In fact, such structures are 14 kJ/mol more stable than structures with three hydride ions, showing that pure DFT functionals give energetically most favorable structures in agreement with experiments. An important reason for this finding is that we have identified a new type of broken-symmetry state that involves only two Fe ions with minority spin, in contrast to the previously studied states with three Fe ions with minority spin. The energetically best structures have the two hydride ions on different faces of the FeMo cluster, whereas better agreement with ENDOR data is obtained if they are on the same face; such structures are only 6–22 kJ/mol less stable.

Efficient Electronic Structure to Stabilize N2‐Bridged Dinuclear Complexes Intended for N2 Activation: Iminophosphorane Iron(I) and Cobalt(I)

We examined the stability of the N2‐ligated mononuclear and N2‐bridged dinuclear complexes for FeI and CoI with the tridentate iminophosphorane ligand, which are in potentially deactivated state for catalytic N2 fixation processes, using density functional theory (DFT) method. The calculated Gibbs free energies of the N2 binding and N2‐bridge formation reactions show that the N2‐bridged FeI‐dinuclear complex is more favorable than the N2 FeI‐mononuclear complex in contrast to the CoI‐mononuclear complexes, which is only the available complex, even if at –80 °C. The stability of the N2‐bridged dinuclear metal complexes has a close relation to the M–N2 bond strength ruled by occupation of the pairs of dπu orbitals, in which the ungerade couples of the dπ orbitals interact with the occupied π orbitals of N2 in antibonding manner. For the catalytic activity of FeI mononuclear complexes, the appropriate order of orbitals to occupy the dπu orbitals is necessary, which is produced by the T‐shaped coordination geometry the ancillary ligands construct.

Understanding of nitrogen fixation electro catalyzed by molybdenum–iron carbide through the experiment and theory

The electrochemical method is considered being a sustainable alternative to the industrial Haber-Bosch process (150–350 atm, 350–550 °C) because it can produce ammonia (NH3) from nitrogen (N2) and water (H2O) at room temperature and pressure. However, since the N≡N triple bond in N2 is one of the strongest bonds in nature, it requires a more negative potential for N2 reduction, which often leads to violent hydrogen evolution reaction (HER) in aqueous electrolysis systems. Therefore, it is a great challenge for the electrocatalytic N2 reduction reaction (ENRR) to find catalysts that can reduce the energy barrier of N2 fixation and inhibit the HER. Herein, inspired by the Mo–Fe site in the biological nitrogenase, we found that the catalyst containing Mo3Fe3C active material has excellent N2-fixing catalytic performance and can effectively inhibit the HER. At −0.05 V vs RHE, the Faraday efficiency (FE) of ENRR was as high as 27.0%. In addition, we innovatively used the Fourier-transformed alternating current voltammetry (FTACV) to explore the electron transfer process in ENRR, indicating that Mo3Fe3C is more conducive to reducing N2 at low potential. According to density functional theory (DFT) calculations, compared with Mo2C and Fe3C, Mo3Fe3C is more helpful in promoting N2 activation and hydrogenation. Due to the synergistic effect of the Mo–Fe site, N2 hydrogenation needs to overcome a lower energy barrier in potential-determining step (PDS). Our research extends the knowledge into bimetallic active sites in ENRR and provides a new insight for the subsequent synthesis of high selectivity catalysts.

Electrochemical Nitrogen Reduction Reaction Performance of Single-Boron Catalysts Tuned by MXene Substrates.

A boron (B) center, which has an electronic structure mimicking the filled and empty d orbitals in transition metals, can effectively activate the triple bond in N2 so as to catalyze the nitrogen reduction reaction (NRR). Here, by means of density functional theory, we have systematically investigated the catalytic performance of a single B atom decorated on two-dimensional transition metal carbides (MXenes). The B-doped Mo2CO2 and W2CO2 MXenes exhibit outstanding catalytic activity and selectivity with limiting potentials of -0.20 and -0.24 V, respectively. Importantly, we have found that, although a high tendency of B-to-adsorbate electron donation can promote the hydrogenation of *N2 to *N2H, it would also severely hamper the *NH2 to *NH3 conversion due to the strong B-N bonding. Such an electron-donation effect can be reasonably tuned by the transition metal in the MXene substrate, which enables us to achieve optimized catalytic performance with a certain moderate degree of electron donation.

Complete cleavage of the N≡N triple bond by Ta2N+ via degenerate ligand exchange at ambient temperature: A perfect catalytic cycle

An unprecedented, spontaneous, and complete cleavage of the triple bond of N2 in the thermal reaction of 15N2 with Ta2 14N+ was observed experimentally by Fourier transform ion cyclotron resonance mass spectrometry; mechanistic aspects of the degenerate ligand exchange were addressed by high-level quantum chemical calculations. The "hidden" dis- and reassembly of N2, mediated by Ta2N+, constitutes a full catalytic cycle. A frontier orbital analysis reveals that the scission of the N2 triple bond is essentially governed by the donation of d-electrons from the 2 metal centers into antibonding π*-orbitals of N2 and by the concurrent migration of electrons from bonding π- and σ-orbitals of N2 into empty d-orbitals of the metals. This work may contribute to a rational design of catalysts in order to reduce the still enormous energy demand required for an artificial dinitrogen activation.

Structural and Reactivity Analyses of Nitrofurantoin–4-dimethylaminopyridine Salt Using Spectroscopic and Density Functional Theory Calculations

Pharmaceutical salt, nitrofurantoin–4-dimethylaminopyridine (NF-DMAP), along with its native components NF and DMAP are scrutinized by FT-IR and FT-Raman spectroscopy along with density functional theory so that an insight into the H-bond patterns in the respective crystalline lattices can be gained. Two different functionals, B3LYP and wB97X-D, have been used to compare the theoretical results. The FT-IR spectra obtained for NF-DMAP and NF clearly validate the presence of C33–H34⋅⋅⋅O4 and N23–H24⋅⋅⋅N9 hydrogen bonds by shifting in the stretching vibration of –NH and –CH group of DMAP+ towards the lower wavenumber side. To explore the significance of hydrogen bonding, quantum theory of atoms in molecules (QTAIM) has been employed, and the findings suggest that the N23–H24⋅⋅⋅N9 bond is a strong intermolecular hydrogen bond. The decrement in the HOMO-LUMO gap, which is calculated from NF → NF-DMAP, reveals that the active pharmaceutical ingredient is chemically less reactive compared to the salt. The electrophilicity index (ω) profiles for NF and DMAP confirms that NF is acting as electron acceptor while DMAP acts as electron donor. The reactive sites of the salt are plotted by molecular electrostatic potential (MEP) surface and calculated using local reactivity descriptors.

QM/MM Study of the Uracil DNA Glycosylase Reaction Mechanism: A Competition between Asp145 and His148.

Uracil DNA glycosylase catalyzes the N-glycosidic bond cleavage of uracil, thereby initiating the base excision repair mechanism for this DNA lesion. Here we employ hybrid quantum mechanics/molecular mechanics calculations to investigate the exact mechanism of the nucleophile attack and the role of the conserved His148 residue. Our calculations suggest that the C1'-N1 bond dissociation proceeds by a migration of the electrophilic sugar in the direction of the water nucleophile, resulting in a planar, oxocarbenium-like transition state. The subsequent nucleophile addition and proton transfer to a nearby base occur without a barrier. We assign the role of a proton acceptor to His148 and elucidate why mutations of this residue curtail the enzymatic activity but do not fully suppress it.

Theoretical prediction of Ni(I)-catalyst for hydrosilylation of pyridine and quinoline.

Catalytic synthesis of dihydropyridine by transition-metal complex is one of the important research targets, recently. Density functional theory calculations here demonstrate that nickel(I) hydride complex (bpy)NiI H (bpy = 2,2'-bipyridine) 1 is a good catalyst for hydrosilylation of both quinoline and pyridine. Two pathways are possible; in path 1, substrate reacts with 1 to form stable intermediate Int1. After that, N3 ─C1 bond of substrate inserts into Ni─H bond of 1 via TS1 to afford N-coordinated 1,2-dihydroquinoline Int2 with the Gibbs activation energy (ΔG°‡ ) of 21.8 kcal mol-1 . Then, Int2 reacts with hydrosilane to form hydrosilane σ-complex Int3; this is named path 1A. In the other route (path 1B), Int1 reacts with phenylsilane in a concerted manner via hydride-shuttle transition state TS2 to afford Int3. In TS2, Si atom takes hypervalent trigonal bipyramidal structure. Formation of hypervalent structure is crucial for stabilization of TS2 (ΔG°‡ = 17.3 kcal mol-1 ). The final step of path 1 is metathesis between Ni─N3 bond of Int3 and Si─H bond of PhSiH3 to afford N-silylated 1,2-dihydroproduct and regenerate 1 (ΔG°‡ = 4.5 kcal mol-1 ). In path 2, 1 reacts with hydrosilane to form Int5, which then forms adduct Int6 with substrate through Si-N interaction between substrate and PhSiH3 . Then, N-silylated 1,2-dihydroproduct is produced via hydride-shuttle transition state TS5 (ΔG°‡ = 18.8 kcal mol-1 ). The absence of N-coordination of substrate to NiI in TS5 is the reason why path 2 is less favorable than path 1B. Quinoline hydrosilylation occurs more easily than pyridine because quinoline has the lowest unoccupied molecular orbital at lower energy than that of pyridine. © 2019 Wiley Periodicals, Inc.

Theoretical Charge density Proof of N–N weak bonds of RDX Energetic Molecule

The bond topological analysis of Cyclotrimethylene-trinitramine (RDX) energetic molecule has been carried out for the wave function obtained from the ab initio and DFT methods of quantum chemical calculations. The geometrical parameters of all bonds are compared with that of experimental reports. The inclusion of diffuse function in HF basis set levels makes the significant shift of bond critical point towards carbon atoms of C–N bonds. The heteroatomic bond density character is well understood from unequal C-cp and cp-N distances in all C–N bonds. For all the level of calculations, the maximum bond density was found for all N=O bonds, attributes the maximum potential energy V(r). The N–N bond properties are strongly depends upon the equilibrium bond length which clears from charge concentration in shorter N1–N4 bond and charge depletion found in longer N2–N5 and N3–N6 bonding regions. The bond topological analysis of all bonds in RDX molecule resulted that the N–N bond is the weakest among all the other bonds. The weakness of N2–N5 and N3–N6 bonds than N1–N4 bond of RDX has also been analyzed from energy density calculation from various level of theories as an alternate for Laplacian of electron density. From the analysis of CHELPG charges at the MP2 level, the N–N bonds of RDX appears to have a significant ionic nature which attributes strong hyperconjugation effect. The hyperconjugation effect of RDX, due to polarization of N–N bonds, is the additional proof of weak N–N bonds in RDX explosive. The isosurface electrostatic potential shows the electro positive and negative region in the molecule. A large negative potential found at the vicinity of oxygen atoms.

Reaction Mechanism for the N-Glycosidic Bond Cleavage of 5-Formylcytosine by Thymine DNA Glycosylase.

Thymine DNA glycosylase (TDG) initiates the base excision repair mechanism for the deamination and oxidation products of cytosine and 5-methylcytosine. This enzyme has a key role in epigenetic regulation, and its catalytic inactivation results in, e.g., mice embryo lethality. Here, we employ molecular dynamics simulations and quantum mechanics/molecular mechanics calculations to investigate the reaction mechanism of the TDG-catalyzed N-glycosidic bond hydrolysis of the modified base 5-formylcytosine. Our results reveal a reaction pathway, which in its first step features a reorganization of the substrate that lowers the barrier height for the subsequent C1'-N1 bond dissociation. The suggested mechanism is consistent with the experimental data, as it is not acid-catalyzed and proceeds through an oxocarbenium-like transition state. It also provides insights into the catalytic roles of the Thr197 and Asn140 residues.

Dinitrogen Activation and Functionalization using β-Diketiminate Iron Complexes.

Iron catalysts are adept at breaking the N-N bond of N2, as exemplified by the iron-catalyzed Haber-Bosch process and the iron-containing clusters at the active sites of nitrogenase enzymes. This Minireview summarizes recent work that has identified a well-characterized set of multi-iron complexes that are capable of breaking and functionalizing N2, and are amenable to detailed mechanistic studies. We discuss the redox balancing, the potential intermediates during N2 activation, the variation of alkali metal reductant, the reversibility of N2 cleavage, and the formation of N-H and N-C bonds from N2.

Easy synthesis and crystal structure of a novel ortho hydroxyl Schiff base compound CH2—{cyclo-C6H10)—NCH—C6H4—OH-2}2

A one-pot and neat reaction procedure is used for the synthesis of CH2—{cyclo-C6H10)—NCH—C6H4—OH-2}2. 1H NMR shows a mixture of ZE and EE isomers in a ratio of 2:0.9. The EE isomer is easily isolated as crystals suitable for the X-ray analysis. 1H,13C NMR and UV-visible spectra of the title compound are studied in different solvents. The crystal structure shows intramolecular H bonds as an EE isomer. The molecule lies about a twofold symmetry axis, passing through the C1 atom. The cyclo-hexyl ring C2—7 shows a chair conformation, with both C2—C1 and C5—N1 bonds in equatorial orientations. The phenolic hydrogen atom H1a forms a good hydrogen bond with the imino nitrogen atom N1 and the N1—C8 bond is short, as expected for a double bond (1.265(4) Å).

Biosynthetically Inspired Transformation of Iboga to Monomeric Post-iboga Alkaloids

Summary Organisms have evolved to produce various natural products from a common precursor as a means of maximizing the number of secondary metabolites, thus acquiring selectional advantages. By adopting nature's divergent biosynthetic strategy, we transformed (+)-catharanthine to various iboga and post-iboga alkaloids, including (−)-conodusine A, (+)-conodusines B and C, (−)-voatinggine, (−)-tabertinggine, and (+)-dippinine B. Well-orchestrated oxidations and reorganizations of catharanthine derivatives enabled chemical access to these natural products.

Configurational and Conformational Equilibria of N6-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG) Lesion in DNA.

The most common lesion in DNA occurring due to clinical treatment with Temozolomide or cellular exposures to other methylating agents is 7-methylguanine (N7-Me-dG). It can undergo a secondary reaction to form N6-(2-deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG). MeFapy-dG undergoes epimerization in DNA to produce either α or β deoxyribose anomers. Additionally, conformational rotation around the formyl bond, C5- N5 bond, and glycosidic bond may occur. To characterize and quantitate the mixture of these isomers in DNA, a 13C-MeFapy-dG lesion, in which the CH3 group of the MeFapy-dG was isotopically labeled, was incorporated into the trimer 5'-TXT-3' and the dodecamer 5'-CATXATGACGCT-3' (X = 13C-MeFapy-dG). NMR spectroscopy of both the trimer and dodecamer revealed that the MeFapy-dG lesion exists in single strand DNA as ten configurationally and conformationally discrete species, eight of which may be unequivocally assigned. In the duplex dodecamer, the MeFapy-dG lesion exists as six configurationally and conformationally discrete species. Analyses of NMR data in the single strand trimer confirm that for each deoxyribose anomer, atropisomerism occurs around the C5- N5 bond to produce R a and S a atropisomers. Each atropisomer exhibits geometrical isomerism about the formyl bond yielding E and Z conformations. 1H NMR experiments allow the relative abundances of the species to be determined. For the single strand trimer, the α and β anomers exist in a 3:7 ratio, favoring the β anomer. For the β anomer, with respect to the C5- N5 bond, the R a and S a atropisomers are equally populated. However, the Z geometrical isomer of the formyl moiety is preferred. For the α anomer, the E- S a isomer is present at 12%, whereas all other isomers are present at 5-7%. DNA processing enzymes may differentially recognize different isomers of the MeFapy-dG lesion. Moreover, DNA sequence-specific differences in the populations of configurational and conformational species may modulate biological responses to the MeFapy-dG lesion.

Using protonation to change a Cl⋯N halogen bond in N-Base:ClOH complexes to a Cl⋯O halogen bond

Ab initio MP2/aug′-cc-pVTZ calculations demonstrate that protonation of N-Base:ClOH complexes at O leads to complexes (N-Base-Cl)+:OH2, as a traditional N⋯Cl halogen bond is replaced by a chlorine-transferred Cl⋯O bond. For a fixed base, the binding energies of the latter complexes are more than an order of magnitude greater than the former. As a function of the ClN distance, EOM-CCSD ClN coupling constants show the evolution of the traditional halogen bond in the N-Base:ClOH complexes, to a chlorine-shared halogen bond in N2:ClOH2+, to a covalent bond in (N-Base-Cl)+:OH2. 1J(ClN) values for these complexes resemble 1J(ClN) for the ions (N-Base-Cl)+.

A theoretical study on excited state proton transfer in 2‐(2′‐dihydroxyphenyl) benzoxazole

AbstractThis research investigates the dynamic excited state process for a novel system 2‐(2′‐dihydroxyphenyl) benzoxazole (DHBO) for excited state proton transfer (ESPT) process based on density functional theory (DFT) and time‐dependent DFT (TDDFT) methods. Because 2 intramolecular hydrogen bonds (O1―H2···N3 and O4―H5···O6) in DHBO molecules may trigger proton transfer process in the S1 state, we focus on these 2 hydrogen bonds. Our results show that only the O1―H2···N3 bond has obvious changes in both bond length and bond angle upon photoexcitation. Charge redistribution also confirms that hydrogen bond wire (O1―H2···N3) is the best way to achieve the ESPT process in the S1 state. Considering the ESPT mechanism, our theoretical potential energy curves of DHBO indicate that only the excited state single‐proton transfer process occurs via O1―H2···N3 rather than O4―H5···O6. We believe that our work not only clarifies the excited state dynamical behavior of DHBO but also promotes the investigations about ESPT reactions in intramolecular or intermolecular hydrogen bonded chemical systems.

Synthesis and structural characterization of a 8-hydroxyquinoline derivative coordinated to Zn(II)

In this work, a 8-hydroxyquinoline derivative, named 8-hydroxyquinoline-2-carboxaldehyde 2-furoyl hydrazone (HQFUH), was obtained. The respective compound was successfully synthesized as well as its respective Zn(II) coordination compound. Both compounds were structurally characterized, by experimental and theoretical IR and Raman spectra, XRD. Single crystal XRD showed that Zn(II) adopts a tetrahedral geometry, in which the neutral chelating ligand coordinates bidentaded by two N-atoms and the neutrality charge is achieved by two coordinated chloride ions. Topological analysis using Quantum Theory of Atoms in Molecules (QTAIM) was performed to investigate ligand interaction through O-atoms. This investigation is important regarding the determination of complex formation constant. The crystal structures of the ligand and complex are arranged according to an orthorhombic system with P212121 and Aea2 space groups, respectively. Ligand displays a E configuration around to C10 = N2 bond, while after the coordination of metal, a Z configuration is observed. Besides molecular structure description of complex, the intermolecular environment was analyzed by Hirshfeld Surface.

Elaborating a new excited state intramolecular proton transfer (ESPT) mechanism for a new π-conjugated dye 2, 2′-((5-(2-(4-methoxyphenyl)ethenyl)-benzene-1,1-diyl)-bis-(nitrilomethylylidene)-diphenol)

In this work, the excited state dynamical behavior of a novel π-conjugated dye 2,2′-((5-(2-(4-methoxyphenyl)ethenyl)-benzene-1,1-diyl)-bis-(nitrilomethylylidene)-diphenol) (C1) has been investigated. Two intramolecular hydrogen bonds of C1 are tested to pre-existing in the ground state via AIM and reduced density gradient. Using a time-dependent density functional theory (TDDFT) method, it has been substantiated that the intramolecular hydrogen bonds of C1 should be strengthened in the S1 state via analyzing fundamental bond length, bond angles, and corresponding infrared vibrational modes. The most obvious variation of these two hydrogen bonds is the O4–H5···N6 bond, which might play important roles in excited state behavior for the C1 system. Furthermore, based on electronic excitation, charge transfer could occur. Just due to this kind of charge re-distribution, two hydrogen bonds should be tighter in the first excited state, which is consistent with the variation of hydrogen bond lengths. Thus, the phenomenon of charge transfer is reasonable evidence for confirming the occurrence of the excited state proton transfer (ESPT) process in the S1 state. Our theoretically constructed potential energy surfaces of C1 show that excited state single proton transfer should occur along with the O4–H5···N6 hydrogen bond rather than the O1–H2···N3 bond. We not only clarify the ESIPT mechanism for C1 but put forward new affiliation and explain a previous experiment successfully.

Redox-switchable structures and NLO property: Li2 doped into the cavity of pyridine helix

Abstract Helical structure was ubiquitous in the nature and many chemists were attracted to synthesize various helicates, to obtain more fantastic functional materials. In this work, we designed pyridine helical ligand with Li2 doped and explored the effects of redox process on its NLO property. All results stressed the control of redox switch on Li2-doped helical complex. In the aspect of geometric structural traits, obtaining or losing electrons made the helix shrank or extended like a coil spring. In the aspect of NLO property, the sharp fluctuation of βtot values with the range of 1.88 × 102 to 7.73 × 106 au indicated that redox process was an effective switch to control the on-off NLO response. According to the two-level formula, the variation of Δμ qualitatively explained the change of βtot. In terms of bonding traits, NBO and AIM analyses showed in the redox process, NBO charge transferred along reversed direction for oxidation and reduction process. The results of E2 and WBIs obtained by population analysis and the properties at Li N BCPs via AIM analysis, including ρ(r), ∇ 2 ρ(r) and H(r) suggested that in the process of obtaining electrons, Li1 N1 bond became weaker while Li1 N3 bond became stronger. All of the results suggested that obtaining or losing electrons was an effective switch to tune the peculiarities of the complex.